The invention provides a multiple missile collaborative ballistic planning method to deal with penetration. The method comprises the specific steps that step 1, based on the radar equation, a radar threat quantification model is established to describe the threat of a radar detection area to a missile; step 2, a collaborative control model is established, the collaborative control model comprisesa collaborative time control model and a collaborative angle control model; step 3, a collaborative attack problem is converted into a nonlinear optimal control problem which is solved based on a hp-self adaptive Radau pseudospectral method, which means at one moment of the flight, the remaining flight time of each missile is determined, whether or not a collaboration is necessary, if necessary, the time for the collaborative attack is calculated and the missile to be adjusted is determined, and the collaborative ballistic planning is conducted on the missile needs to be adjusted. According tothe multiple missile collaborative ballistic planning method, multiple missiles attacking a target on the same attacking time and with the same attacking angle is ensured; meanwhile, the radar detection threat is smallest during the flight, and the comprehensive combat effectiveness is effectively improved.